Browsing by Author "Cunha, Regina L."
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- Comparative mitogenomic analyses and gene rearrangements reject the alleged polyphyly of a bivalve genusPublication . Cunha, Regina L.; Nicastro, Katy; Zardi, Gerardo I.; Madeira, Celine; McQuaid, Christopher D.; J. Cox, Cymon; Castilho, RitaBackground: The order and orientation of genes encoded by animal mitogenomes are typically conserved, although there is increasing evidence of multiple rearrangements among mollusks. The mitogenome from a Brazilian brown mussel (hereafter named B1) classified as Perna perna Linnaeus, 1758 and assembled from Illumina short-length reads revealed an unusual gene order very different from other congeneric species. Previous mitogenomic analyses based on the Brazilian specimen and other Mytilidae suggested the polyphyly of the genus Perna. Methods: To confirm the proposed gene rearrangements, we sequenced a second Brazilian P. perna specimen using the "primer-walking" method and performed the assembly using as reference Perna canaliculus. This time-consuming sequencing method is highly effective when assessing gene order because it relies on sequentially-determined, overlapping fragments. We also sequenced the mitogenomes of eastern and southwestern South African P. perna lineages to analyze the existence of putative intraspecific gene order changes as the two lineages show overlapping distributions but do not exhibit a sister relationship. Results: The three P. perna mitogenomes sequenced in this study exhibit the same gene order as the reference. CREx, a software that heuristically determines rearrangement scenarios, identified numerous gene order changes between B1 and our P. perna mitogenomes, rejecting the previously proposed gene order for the species. Our results validate the monophyly of the genus Perna and indicate a misidentification of B1.
- Divergence and gene flow history at two large chromosomal inversions underlying ecotype differentiation in the long‐snouted seahorsePublication . Meyer, Laura; Barry, Pierre; Riquet, Florentine; Foote, Andrew; Der Sarkissian, Clio; Cunha, Regina L.; Arbiol, Christine; Cerqueira, Frédérique; Desmarais, Erick; Bordes, Anaïs; Bierne, Nicolas; Guinand, Bruno; Gagnaire, Pierre‐AlexandreChromosomal inversions can play an important role in divergence and reproductive isolation by building and maintaining distinct allelic combinations between evolutionary lineages. Alternatively, they can take the form of balanced polymorphisms that segregate within populations until one arrangement becomes fixed. Many questions remain about how inversion polymorphisms arise, how they are maintained over the long term, and ultimately, whether and how they contribute to speciation. The long-snouted seahorse (Hippocampus guttulatus) is genetically subdivided into geographic lineages and marine-lagoon ecotypes, with shared structural variation underlying lineage and ecotype divergence. Here, we aim to characterize structural variants and to reconstruct their history and suspected role in ecotype formation. We generated a near chromosome-level genome assembly and described genome-wide patterns of diversity and divergence through the analysis of 112 whole-genome sequences from Atlantic, Mediterranean, and Black Sea populations. By also analysing linked-read sequencing data, we found evidence for two chromosomal inversions that were several megabases in length and showed contrasting allele frequency patterns between lineages and ecotypes across the species range. We reveal that these inversions represent ancient intraspecific polymorphisms, one likely being maintained by divergent selection and the other by pseudo-overdominance. A possible selective coupling between the two inversions was further supported by the absence of specific haplotype combinations and a putative functional interaction between the two inversions in reproduction. Lastly, we detected gene flux eroding divergence between inverted alleles at varying levels for the two inversions, with a likely impact on their dynamics and contribution to divergence and speciation.
- Evolution at a different pace: distinctive phylogenetic patterns of cone snails from two ancient oceanic archipelagosPublication . Cunha, Regina L.; Lima, Fernando P.; Tenorio, Manuel J.; Ramos, Ana A.; Castilho, Rita; Williams, Suzanne T.Ancient oceanic archipelagos of similar geological age are expected to accrue comparable numbers of endemic lineages with identical life history strategies, especially if the islands exhibit analogous habitats. We tested this hypothesis using marine snails of the genus Conus from the Atlantic archipelagos of Cape Verde and Canary Islands. Together with Azores and Madeira, these archipelagos comprise the Macaronesia biogeographic region and differ remarkably in the diversity of this group. More than 50 endemic Conus species have been described from Cape Verde, whereas prior to this study, only two nonendemic species, including a putative species complex, were thought to occur in the Canary Islands. We combined molecular phylogenetic data and geometric morphometrics with bathymetric and paleoclimatic reconstructions to understand the contrasting diversification patterns found in these regions. Our results suggest that species diversity is even lower than previously thought in the Canary Islands, with the putative species complex corresponding to a single species, Conus guanche. One explanation for the enormous disparity in Conus diversity is that the amount of available habitat may differ, or may have differed in the past due to eustatic (global) sea level changes. Historical bathymetric data, however, indicated that sea level fluctuations since the Miocene have had a similar impact on the available habitat area in both Cape Verde and Canary archipelagos and therefore do not explain this disparity. We suggest that recurrent gene flow between the Canary Islands and West Africa, habitat losses due to intense volcanic activity in combination with unsuccessful colonization of new Conus species from more diverse regions, were all determinant in shaping diversity patterns within the Canarian archipelago. Worldwide Conus species diversity follows the well-established pattern of latitudinal increase of species richness from the poles towards the tropics. However, the eastern Atlantic revealed a striking pattern with two main peaks of Conus species richness in the subtropical area and decreasing diversities toward the tropical western African coast. A Random Forests model using 12 oceanographic variables suggested that sea surface temperature is the main determinant of Conus diversity either at continental scales (eastern Atlantic coast) or in a broader context (worldwide). Other factors such as availability of suitable habitat and reduced salinity due to the influx of large rivers in the tropical area also play an important role in shaping Conus diversity patterns in the western coast of Africa.
- Genomics goes deeper in fisheries science: The case of the blackspot seabream (Pagellus bogaraveo) in the northeast AtlanticPublication . Cunha, Regina L.; Robalo, Joana I.; Francisco, Sara M.; Farias, Inês; Castilho, Rita; Figueiredo, IvoneRecent advances in genomics are an essential contributor to the assessment of fish stocks by providing a finescale identification of the species' genetic boundaries. The blackspot seabream, Pagellus bogaraveo, is a commercial sparid distributed across the northeast (NE) Atlantic and the Mediterranean. Within the NE Atlantic, three P. bogaraveo stocks are currently defined: Azores; Atlantic Iberian waters; Celtic Sea and the Bay of Biscay. We used a genotyping-by-sequencing (GBS) approach to better define the spatial scale at which the species occurs in the NE Atlantic. Our findings revealed the existence of an additional genetic cluster in the eastern Atlantic (Gulf of C ' adiz) that was not identified in previous studies based on mitochondrial DNA or microsatellite data. The combined effect of ocean circulation patterns, complex bathymetry and the existence of local upwelling may play an important role on the retention of blackspot seabream larvae and adults, providing an explanation for the genetic differentiation between the specimens caught off the Gulf of C ' adiz and Peniche (Portugal). Results presented here revealed hidden intra-specific genetic differentiation and can inform a finer-scale sampling to determine the new stock boundaries in the Atlantic Iberian coasts.
- Hidden diversity of the olive ridley sea turtle (Lepidochelys olivacea) from Angola, West AfricaPublication . Cunha, Regina L.; Costa, Adjany; Godinho, Filipa; Santos, Carmen; Castilho, RitaThe olive ridley sea turtle (Lepidochelys olivacea) occupies a wide range within the tropical and subtropical areas of the Pacific, Indian, and Southern Atlantic Oceans. Although occurring in large numbers, the IUCN status for this species is "vulnerable" due to existing threats in their nesting sites. We report the first genetic data on L. olivacea from Palmeirinhas-Onca beach, Angola, West Africa. Genetic diversity based on a 400 bp-fragment of the mitochondrial control region of 39 individuals indicated low nucleotide and haplotype diversities compared to other Atlantic populations. We detected a new haplotype present in two individuals from Angola, while the remaining specimens shared a haplotype that is distributed in both sides of the Atlantic and in the Mediterranean, suggesting connectivity between these populations. The baseline data we are generating have a broader significance for characterizing intraspecific biodiversity in the olive ridley sea turtle, which is vital for developing effective conservation policies.
- Phylogeny and diversification patterns among vesicomyid bivalvesPublication . Decker, Carole; Olu, Karine; Cunha, Regina L.; ARNAUD-HAOND, SophieVesicomyid bivalves are among the most abundant and diverse symbiotic taxa in chemosynthetic-based ecosystems: more than 100 different vesicomyid species have been described so far. In the present study, we investigated the phylogenetic positioning of recently described vesicomyid species from the Gulf of Guinea and their western Atlantic and Pacific counterparts using mitochondrial DNA sequence data. The maximum-likelihood (ML) tree provided limited support for the recent taxonomic revision of vesicomyids based on morphological criteria; nevertheless, most of the newly sequenced specimens did not cluster with their morphological conspecifics. Moreover, the observed lack of geographic clustering suggests the occurrence of independent radiations followed by worldwide dispersal. Ancestral character state reconstruction showed a significant correlation between the characters "depth'' and "habitat'' and the reconstructed ML phylogeny suggesting possible recurrent events of 'stepwise speciation' from shallow to deep waters in different ocean basins. This is consistent with genus or species bathymetric segregation observed from recent taxonomic studies. Altogether, our results highlight the need for ongoing re-evaluation of the morphological characters used to identify vesicomyid bivalves.
- Three mitochondrial lineages and no Atlantic-Mediterranean barrier for the bogue Boops boops across its widespread distributionPublication . Cunha, Regina L.; Faleh, Abderraouf Ben; Francisco, Sara; Šanda, Radek; Vukić, Jasna; Corona, Luana; Dia, Mamadou; Glavičić, Igor; Kassar, Abderrahmane; Castilho, Rita; Robalo, Joana I.Marine species exhibiting wide distributional ranges are frequently subdivided into discrete genetic units over limited spatial scales. This is often due to specific life-history traits or oceanographic barriers that prevent gene flow. Fine-scale sampling studies revealed distinct phylogeographic patterns in the northeastern Atlantic and the Mediterranean, ranging from panmixia to noticeable population genetic structure. Here, we used mitochondrial sequence data to analyse connectivity in the bogue Boops boops throughout most of its widespread distribution. Our results identified the existence of three clades, one comprising specimens from the Azores and eastern Atlantic/Mediterranean, another with individuals from the Canary Islands, Madeira and Cape Verde archipelagos, and the third with samples from Mauritania only. One of the branches of the northern subtropical gyre (Azores Current) that drifts towards the Gulf of Cadiz promotes a closer connection between the Azores, southern Portugal and the Mediterranean B. boops populations. The Almeria-Oran Front, widely recognised as an oceanographic barrier for many organisms to cross the Atlantic-Mediterranean divide, does not seem to affect the dispersal of this benthopelagic species. The southward movement of the Cape Verde Frontal Zone during the winter, combined with the relatively short duration of the pelagic larval stage of B. boops, may be potential factors for preventing the connectivity between the Atlantic oceanic archipelagos and Mauritania shaping the genetic signature of this species.
- Uncovering the shell game with barcodes: diversity of meiofaunal Caecidae snails (Truncatelloidea, Caenogastropoda) from Central AmericaPublication . Egger, Christina; Neusser, Timea P.; Norenburg, Jon; Leasi, Francesca; Buge, Barbara; Vannozzi, Angelo; Cunha, Regina L.; Cox, Cymon J.; Jörger, Katharina M.Caecidae is a species-rich family of microsnails with a worldwide distribution. Typical for many groups of gastropods, caecid taxonomy is largely based on overt shell characters. However, identification of species using shell characteristics is problematic due to their rather uniform, tubular shells, the presence of different growth stages, and a high degree of intraspecific variability. In the present study, a first integrative approach to caecid taxonomy is provided using light-microscopic investigation with microsculptural analyses and multi-marker barcoding, in conjunction with molecular species delineation analyses (ABGD, haplotype networks, GMYC, and bPTP). In total 132 specimens of Caecum and Meioceras collected during several sampling trips to Central America were analyzed and delineated into a minimum of 19 species to discuss putative synonyms, and supplement the original descriptions. Molecular phylogenetic analyses suggest Meioceras nitidum and M. cubitatum should be reclassified as Caecum, and the genus Meioceras might present a junior synonym of Caecum. Meiofaunal caecids morphologically resembling C. glabrum from the Northeast Atlantic are a complex of cryptic species with independent evolutionary origins, likely associated with multiple habitat shifts to the mesopsammic environment. Caecum invisibile Egger & Jörger, sp. nov. is formally described based on molecular diagnostic characters. This first integrative approach towards the taxonomy of Caecidae increases the known diversity, reveals the need for a reclassification of the genus Caecum and serves as a starting point for a barcoding library of the family, thereby enabling further reliable identifications of these taxonomically challenging microsnails in future studies.
- Wandering behaviour prevents inter and intra oceanic speciation in a coastal pelagic fishPublication . Silva, Goncalo; Cunha, Regina L.; Ramos, Ana; Castilho, RitaSmall pelagic fishes have the ability to disperse over long distances and may present complex evolutionary histories. Here, Old World Anchovies (OWA) were used as a model system to understand genetic patterns and connectivity of fish between the Atlantic and Pacific basins. We surveyed 16 locations worldwide using mtDNA and 8 microsatellite loci for genetic parameters, and mtDNA (cyt b; 16S) and nuclear (RAG1; RAG2) regions for dating major lineage-splitting events within Engraulidae family. The OWA genetic divergences (0-0.4%) are compatible with intra-specific divergence, showing evidence of both ancient and contemporary admixture between the Pacific and Atlantic populations, enhanced by high asymmetrical migration from the Pacific to the Atlantic. The estimated divergence between Atlantic and Pacific anchovies (0.67 [0.53-0.80] Ma) matches a severe drop of sea temperature during the Gunz glacial stage of the Pleistocene. Our results support an alternative evolutionary scenario for the OWA, suggesting a coastal migration along south Asia, Middle East and eastern Africa continental platforms, followed by the colonization of the Atlantic via the Cape of the Good Hope.